vegemite {vegan} | R Documentation |
The function prints a compact vegetation table, where species are rows, and each site takes only one column without spaces. The vegetation table can be ordered by explicit indexing, by environmental variables or results from an ordination or cluster analysis.
vegemite(x, use, scale, sp.ind, site.ind, zero=".", select ,...) coverscale(x, scale=c("Braun.Blanquet", "Domin", "Hult", "Hill", "fix","log"), maxabund)
x |
Vegetation data. |
use |
Either a vector, or an object from cca ,
decorana etc. or hclust or a
dendrogram for ordering sites and species. |
sp.ind |
Species indices. |
site.ind |
Site indices. |
zero |
Character used for zeros. |
select |
Select a subset of sites. This can be a logical vector
(TRUE for selected sites), or a vector of indices of selected
sites. The order of indices does not influence results, but you
must specify use or site.ind to reorder sites.
|
scale |
Cover scale used (can be abbreviated). |
maxabund |
Maximum abundance used with scale = "log" .
Data maximum in the select ed subset will be usd if this is
missing. |
... |
Arguments passed to coverscale (i.e., maxabund ). |
The function prints a traditional vegetation table. Unlike in ordinary data matrices, species are used as rows and sites as columns. The table is printed in compact form: only one character can be used for abundance, and there are no spaces between columns. Species with no occurrences are dropped from the table.
The parameter use
can be a vector or an object from
hclust
, a dendrogram
or any ordination
result recognized by scores
(all ordination methods in
vegan and some of those not in vegan).
If use
is a vector, it is used
for ordering sites. If use
is an object from ordination, both
sites and species are arranged by the first axis.
When use
is an
object from hclust
or a dendrogram
, the
sites are ordered similarly
as in the cluster dendrogram.
If ordination methods provide species scores, these are used for
ordering species. In all cases where species scores are missing,
species are ordered by their weighted averages (wascores
)
on site scores. There is no natural, unique ordering in hierarchic
clustering, but in some cases species are still nicely ordered (please
note that you can reorder.dendrogram
to have such a
natural order).
Alternatively, species and sites can be ordered explicitly giving
their indices or names in parameters sp.ind
and
site.ind
. If these are given, they take precedence over
use
. A subset of sites can be displayed using argument
select
, but this cannot be used to order sites, but you still
must give use
or site.ind
.
If scale
is given, vegemite
calls
coverscale
to transform percent cover
scale or some other scales into traditional class scales used in
vegetation science (coverscale
can be called directly, too).
Braun-Blanquet and Domin scales are actually not
strict cover scales, and the limits used for codes r
and
+
are arbitrary. Scale Hill
may be
inappropriately named, since Mark O. Hill probably never intended this
as a cover scale. However, it is used as default 'cut levels' in his
TWINSPAN
, and surprisingly many users stick to this default,
and this is a de facto standard in publications. All
traditional
scales assume that values are cover percentages with maximum 100.
However, non-traditional alternative log
can be used with any
scale range. Its class limits are integer powers of 1/2 of the
maximum (argument maxabund
), with +
used for non-zero entries
less than 1/512 of the maximum (log
stands alternatively for
logarithmic or logical). Scale fix
is intended for `fixing'
10-point scales: it truncates scale values to integers, and replaces
10 with X
and positive values below 1 with +
.
The function is used mainly to print a table, but it returns (invisibly) a list with items:
species |
Ordered species indices |
sites |
Ordered site indices |
These items can be used as arguments sp.ind
and site.ind
to reproduce the table. In addition to the proper table, the function
prints the numbers of species and sites and the name of the used cover
scale at the end.
This function was called vegetab
in older versions of
vegan
. The new name was chosen because the output is so
compact (and to avoid confusion with the vegtab
function in the
labdsv package).
Jari Oksanen
The cover scales are presented in many textbooks of vegetation science; I used:
Shimwell, D.W. (1971) The Description and Classification of Vegetation. Sidgwick & Jackson.
cut
and approx
for making your own
`cover scales', wascores
for weighted averages.
data(varespec) ## Print only more common species freq <- apply(varespec > 0, 2, sum) vegemite(varespec, scale="Hult", sp.ind = freq > 10) ## Order by correspondence analysis, use Hill scaling and layout: dca <- decorana(varespec) vegemite(varespec, dca, "Hill", zero="-") ## Show one class from cluster analysis, but retain the ordering above clus <- hclust(vegdist(varespec)) cl <- cutree(clus, 3) sel <- vegemite(varespec, use=dca, select = cl == 3, scale="Br") # Re-create previous vegemite(varespec, sp=sel$sp, site=sel$site, scale="Hult")